The Waking Sleeper
by Lupin the Vapour
Summary: Not long after the X Parasite incident, bounty hunter Samus Aran is sent out on a mission to collect one of history's greatest warriors, the legendary Spartan 117.
1. Prologue

Commander Striek sighed heavily as he stood with his back to Aurora Unit 1327, "Are you sure it's him?"

The large organic computer responded in their typical manner, "Indeed, we have a ninety seven percent confirmation on the identity of the life signs. It appears that the subject has been in deep cryo sleep since the Ark incident, putting it at several hundred years since initial freezing. Based on our historic records of his genetic manipulation, he should have been able to survive relatively unharmed, though we offer no guarantee."

Striek nodded, narrowing his dark eyes, "Well, we could use all the help we can get, and he sure as hell is quite a bit of it, if his records aren't made up to hype him up as a hero. Send in a squad to retrieve him."

"Sir, if we may, it would be more advisable to send a single, capable military unit, as the wreck is located deep in Kriken space. Might we suggest Samas Aran?"

The commander grunted, "She's still recovering from the X Parasite incident. The cure she was given has been mutating, and we don't know how stable she is."

"We have been observing her closely, and we believe she is ready for a mission."

"Very well, send word to her. It's time to bring in Sierra 117."


	2. File One: Retrieval

File restricted to access level Omega unless successful in retrieval.  
>Samus Aran<br>Mission Log  
>Objective: Retrievedestroy subject codenamed Sierra 117 from Krikin space undetected

Entry start  
>I have been instructed to keep a log of my progress to ensure that the Metroid vaccine and the X Parasites that still inhabit my body do not begin deteriorating my mind. It has been theorized by some of the same scientists that first developed the vaccine that it could, in time, mutate my mind, eventually making my physiology and mentality that of a humanoid Metroid entirely. It has already given me several of their abilities, along with their weaknesses. The final X Parasite that I absorbed made me temporarily immune to the cold weakness that the Metroid DNA had given me, but it has come back with a vengeance. In addition, I can no longer safely take off even my helmet without risking taking skin with it, as my body has fully fused to the suit itself. Fortunately, the vaccine has replaced my need for actual food with a hunger for energy and a method to absorb it. I now understand why the Metroids would lunge at any viable life force signature, as I have now developed the "smell" for the energies around me. Even now, I have to restrain myself from draining the power core of the ship I am flying in, and a life force signature is to these power cores what a delicately prepared high class meal would be to a flash frozen ration. Cravings aside, these new mutations have the potential to be highly beneficial to missions, as my normal motion detector has a tendency to be jammed by some of the more cunning of the subjects that I have to track down. I find myself especially grateful for it given the Kriken propensity for stealth and ranged combat. Their natural cloaking ability may fool eyes, and their uncanny ability to remain perfectly motionless may fool motion trackers, but they still possess an energy signature, and while that can be suppressed to hide from electronic scanners, the Metroid's "smell" can still find it.<p>

As for the mission itself, I have researched the subject fairly extensively, and, while I am slightly skeptical as to the accuracy of the exploits detailed within, I am reminded that my own exploits are largely believed to be crafted of fiction due to their immensities, so I will not rule out their plausibility entirely. It has also been brought to my attention that an older model of AI was with the subject at time of loss, and it is potentially still there. These older models tended to have a fairly short half-life when compared to the lifespans of the ones that we have now, but the reports say that this model was different in more ways than one. It is, therefore, possible that it found some way to survive the long hibernation, so the variable of subject Cortana is still on the table. The data on these types of AI cores hints that they become erratic as they near the end of their half-life, and begin to deteriorate in both sanity and function. If it is still functioning, it will be considered a liability with the potential to become an asset. As it is, its data cores should hold some information of historic significance, and should be gathered to give further insight into the various incidents that it was a part of, including what should be the only remaining detailed schematics of the Halo rings that were a part of the incident of the same name.

My ship is currently entering Kriken space, so I will be continuing this log at a later time when I feel it is safe to do so.

* * *

><p>Samus leaned back in her pilot's seat, keeping one eye on her long range motion tracker as she peered out the window, eyes scanning for the telltale distortion that came with Kriken stealth. It was much harder to see out in deep space, but still possible with a trained, and attentive eye. Her right hand wandered to her left palm, rubbing her thumb over the small spike protruding from the suit's surface. The white bone-like structure was covered in tiny black lines leading from the tip down to the base. The bounty hunter had discovered that it was the same structure as the Metroids' jaws, and could be used to syphon energy out of a living object or a machine. She remained like this, all but motionless as the autopilot took her to the site that the remains of the Forward Unto Dawn.<p>

Samus took back manual control of her gunship as the frigate came into sight. She did a few circuits around the wreckage to get a read on the situation. As expected, it was all but completely destroyed. Half the ship looked like it had been sliced off with a giant sword. The side that had been cut, along with a lot of the exterior, was coated in sheets of ice, most likely the result of leaks in the ship over the centuries, and never having been close enough to heat to have thawed out. Samus considered attempting a landing in what appeared to be the cargo bay, but the icy buildup was thicker around that area, making maneuvering the gunship in dangerous. In the end, she settled for using the magnetic landing gear to latch onto the side of the ship where she detected a docking bay.

As the hunter emerged, she activated her grappling beam, pulling herself one swing at a time until she was next to the frozen shut door. With her new sensitivity, even being this close to the ice began wearing on her. Her arm shook slightly as she aimed her arm canon, the plasma beam primed. She quickly melted the obstruction down and promptly used her scanning visor to access the ship's computer, or she attempted to. The ship seemed to be without power, though that was hardly a surprise. She jammed the spike in her hand against the edge of the door, utilizing an ability she had first guessed she may possess by her memories of fighting the Hunter Metroids. She expelled some of her stored energy, though just enough to open the doors. Inside looked to be in a lot better shape, and although the power may have been off, it looked as though the inner door to the airlock hadn't been closed at the time it lost power. She pulled herself inside, looking around to see if she could spot any kind of signs of life. The hunter kept her energy sense on high alert, trying her hardest to detect anything that may have taken up residence in the ship.

The design was typical of ships from the era that this ship had come from. Gunmetal Grey with sparse décor. It was a military vessel, after all. The hunter continued to go through the ship, prying open doors where she could, blasting them in others, and charging them in as few places as possible. Her energy supply was hardly limitless. Finally getting to the middle of the ship, where the cut seemed to be, she began detecting life forms. Multiple, and close. That meant one thing, the Kriken had found the Forward Unto Dawn first. They clearly would know that she was there, and anything she did to try to be stealthy would alert them to the fact that they had been noticed. Kriken one on one were nothing to really be afraid of in close quarters, but there were five of them, and five Kriken meant that they couldn't all be taken down simultaneously. A popular tactic among them was to gang up on one target and all take an attempt at a headshot, all but ensuring at least one would hit its mark, most likely taking the target down in doing so. Samus frowned, this would be tricky.

The panel beside her lit up, to the hunter's surprise, projecting a small blue woman appearing to be covered in old silicone based computer designs. The hunter raised an eyebrow at the figure, who raised her hands, "You're human, excellent. I've been waiting for so long for someone to come. I'm not actually sure how long, I put myself in a hibernation state for most of it. The ship has been going in and out of power with some of the solar panels catching the power from a few stars, but those were never meant to run the entire ship, just alleviate the strain on the engines slightly when near a star. And now we only have a few of them left. I've barely been able to keep the power in our room going, but I've had to to make sure the chief didn't wake early. He's preserved right now, but I didn't want him waking up, and right now, I barely have enough power to keep the system working, which it actually requires considerably more power to open one of those pods than to keep it going for a few minutes. I'll need you to give some inputs when you-"

Samus held a finger to her faceplate, pulling herself over to the panel the figure was projecting from. There was a small keypad on it. She used that to type out "Five life signs detected. Hostile, or friendly?"

The figure looked at her confusedly, "Five? No, there should only be one. And that one should be weakened. I'll do a- Oh, no, you're right. Four figures are against the back of what's left of the room. They seem to know you're here. I can try to distract them, but I'm not sure if that'll work. Tell me when you're ready."

Samus made her way to the door, and got against the wall beside it, her hand on her arm canon. She took a deep breath, glanced at the figure, and gave a short nod. The doors opened, bathing the room with light that had apparently just been turned on. Sure enough, there against the wall were four Kriken warriors, reeling from the sudden flash of light that had clearly been her distraction. She dispatched three with quick use of a missile each, and rushed the final one just as he recovered. She jammed her spike into his chest and pulled. The insectoid shook as his life force ran down the spike, up Samus's arm, and into her core. She closed her eyes, enjoying the bliss of the feeling as the warrior stopped moving. She had discovered the amazing feeling of feeding on a life force by pure accident once with a small rodent, but that was hardly comparable to the full sized being like this. She dropped her victim and turned to look around. There in the wall were several stasis pods. And in one was a green armored human.

* * *

><p>Sorry this took so long, guys. i just didn't have the motivation to write for a while. i'm back, though! Don't worry, this is about as short as my chapters get, i prefer longer ones, generally more than 2.5k words, but i wanted to get this one out before i lost motivation again. Promise i'll be better at updating them more often. Enjoy!<p> 


	3. File Two: Awakening

Hyper incripted data file number 11786

Author: Cortana, UNSCSN CTN 0452-9

Date: Unknown

Location: Charon-Class light frigate UNSC Forward Unto Dawn FFG-201

I detailed in my last log how I have been losing large gaps of time in my memory, and it seems that this trend is continuing. I recovered from my most recent lapse in concentration to find that even more of the ship has frozen over, which is disconcerting, considering that the liquid that would have been escaping was what would have been keeping John alive. Fortunately, however, I also found life signs on the ship again, a seemingly human life sign at that. I initially attempted to contact the newcomer, but the lack of power in most of the ship prevented me from activating any of the com units on the ship. Fortunately, our guest seemed to know where the chief was, which I'm still unsure as to why she didn't just dock and use the hole in the side of the ship.

I'm putting this down as record now because some of this newcomer's actions have started worrying me. I was originally confused by the jolts of electricity that were coursing through the ship. Not enough to really help anything long term, but clearly done with the intention of localized power for individual mechanisms. Then I came to the logical conclusion that it was a machine that the newcomer had that was a kind of jump starter, similar to those used in the twenty first century to help vehicles that had died. Gradually, though, as she drew closer, I realized that it was, in fact, bioelectricity. I was baffled. In the midst of me coming up with likely scenarios, she arrived, and it was revealed that she was able to detect life signs, no doubt how she found John's location. She then proceeded to dispatch three aliens of unknown origin with traditional ballistics explosives and a fourth by, and I record this with the utmost disbelief, draining its life energy into herself.

This was clearly how she was able to use bioelectricity to power the machines around the ship. I hadn't had the time nor power to perform a proper scan, so I wasn't sure up until now, but this is clearly not a human. At least, this is not an unaltered human. I can only hope now that I chose to help the right side of this fight over John's frozen form. I will likely know at least whether she is an assassin soon, as she seems to be attempting to access the Hushed Casket.

* * *

><p>The last thing he remembered was the front of the cryo chamber closing in front of him, preparing him for a long sleep. He had expected to be awoken, perhaps not soon, but before anything overly dire happened. The first thing he saw upon his awakening, however, was not the face of a UNSC marine or even a familiar design for armor. It was the sleek face mask of a power armor suit. The design looked more Covenant than human, but the events leading up to the destruction of the Ark and the stiffness from an extended stay in cryo sleep stayed his gut reaction to enter a combat stance. The helmet and suit had an almost organic appearance to them, though the Spartan had no doubt as to their utility, if not combat readiness. Surely, if this was from either the remnants of the races that had made up the Covenant, it would be the best of the best so as to contain or assist the legend that he had become for them, and the UNSC wouldn't send anyone unskilled to retrieve a Spartan. The armored figure floated in front of the pod for a while, one hand against its temple until John had had enough waiting, "Well? Did I miss anything while I was asleep?" The figure nodded and immediately threw what seemed to be a chain of electricity to pull itself to the door.<p>

A familiar face was watching from the pedestal he had left her, "Chief, over here." It was quick work to jump his way to the podium and put his traveling companion back into his armor's neural network. Once back, he heard a sigh of relief, "Good to be back."

The Chief looked to the door to see their mysterious benefactor waiting and watching, "So, who's this?"

Cortana's voice was clearly exasperated, "I have no idea. I've tried to find out, but she makes you look downright chatty. And trying to tap into her network with the systems I've got access to is about like trying to break into a fortified base with a paper bag. I don't have any idea, but she seems to be working with us for now, and her ship has a UNSC tag, though it's in a strange encryption, and it's not in the normal system of tags. I think she might be a mercenary of some sort."

The Spartan looked back to the exit to the hangar that led into deep space, but ultimately decided to follow the newcomer, "She?"

"Based on body shape and size, that's my best guess. Though I'm not actually sure she's human, so that's about like taking a guess at a fish's gender based on the size and shape of other fish that look like it. She's got more than the typical UNSC gear, as you've probably noticed." The stranger was currently pulling herself along via the energy rope, accenting the point, "Though that was the standard gear when you went to sleep. Most of the gear she has didn't even exist at that time, so clearly we've been out of the picture for quite some time. Longer than I'd planned. I have no idea how long, though, and unless she suddenly develops a love for conversation, I don't think we'll be finding out for a while."

John nodded as they continued their way to the ship's exterior the long way. This time, however, the doors were already open, expediting the process. Once they got to the air lock, the Chief noticed a small purple fighter in a similar style to the mercenary's helmet. Their guide stopped and began pressing seemingly invisible buttons on her arm as John came up beside her, "Our ride?" He only received a nod in return as the ship cruised closer to the wreckage.

The smaller ship docked on the side of the frigate like a spider, one of each of the four "legs" connecting to the armor easily. Cortana let out a slight hum, "If this is UNSC, then it looks like our temporary friendship with the Elites was a little less temporary than we expected. This looks a lot like something they would design." A hatch in the bottom of the ship folded open, allowing the armored stranger to jump inside. John watched her go, and heard Cortana in the back of his head, "Are we sure we should follow her?"

"It's that or stay here. Besides, she seems like she'd be great at parties."

"You always think you're funny first thing in the morning." And with that, the Chief jumped into the air lock.

* * *

><p>Upon arriving in the ship, the Spartan noticed two things. The first was that the cockpit was much covered in much more equipment than the fighters he was used to, and the second was that it was much more colorful. He got the distinct feeling that this wasn't simply an aesthetic choice, however, as he watched the mercenary's hands dance across the machines.<p>

As he watched her work her craft, he put his hand on the back of her seat, causing her to instantly stiffen. She reached up to press a button above her head that had no indicator on it, and the first new voice the Chief had heard since awakening came over the speakers around him, "Please proceed to the passenger bay behind you, 117. The Lady needs to concentrate."

Cortana's voice came a bit puzzled, "An onboard AI in a ship this size? Surely not. What would it even do?"

The voice came back over the speakers, stiff and formal, "Mostly interpersonal affairs and liaisons with the Federation. I occasionally give tactical advisories on situations, and I can auto-pilot the ship when there is need. On a related note, you are an onboard AI for an individual person."

"Fair point. Though this is a very special individual person."

The Spartan spoke up, shaking his head, "Look, not that this isn't great, but I'd like to know why I have to go to the back. I still don't trust you completely yet."

"Well, primarily, there isn't room in the cockpit for you to sit down." The pilot reached up and pressed the button again, "Beyond that, you really should follow the request of your chauffeur." Another press of the button, "I'm trying, Lady, don't get testy."

"At least tell us who we're riding with."

"You are currently riding aboard the gunship of Samus Aran, Bounty Hunter for the Galactic Federation, an intergalactic peacekeeping force that employs both a moderate military force of its own and small, individual units capable of doing great enough feats without access to reinforcements or backup. During your time, it was known as the United Nations Space Command, or UNSC. It has since expanded to include more than just humanity, and is a blanket protector for anyone that abides by the laws they lay down, whether or not they can contribute back to the overall effort. Does that explain it?"

The pilot, Samus Aran, put a hand to her forehead. John noticed the protrusion in the center of her palm, and realized several things at once. Calmly, he nodded to himself, "It'll do for now," and turned to walk back into the passenger bay.

Cortana was slightly incredulous, "You're just going to take their word on it? Just like that? They're clearly hiding something from us, and you're just going to walk into a holding cell? That's not like you."

As the doors sealed behind him, the Chief went to take a seat in the cramped quarters, by far less spacious than the cockpit. This was clearly not meant for full sized human cargo that was not meant for processing, "Aran isn't human. Specifically, she's a predator of some kind."

"Listen, I'm the smart one of the two of us. That has nothing to do with-"

"When I was fighting the Covenant, something I would do with the Jackals was I would use that against them. Make them need to hunt something. Make them lose control. They were always on the verge of a rage at something that wasn't a Jackal. Now think about a solitary hunter. They would have a hard time resisting the urge to hunt anything that moved or breathed. When the AI was saying she had to concentrate, he was telling the temptation to get out of smelling range."

Cortana let out a mocking laugh, "I doubt even with all the gadgets she has, she could beat you."

A voice came over the speakers, "Irrelevant. A fight would damage the cockpit and likely end up with one of the combatants dead. Whichever one it happened to be, it would be a great loss, and then the other would be stranded in the middle of Kriken space. And the Kriken are not friendly to anything not Kriken."

"So, what, we're supposed to just accept that your pilot has bad self-control and go along with whatever she wants?"

"The Lady is currently adjusting to her new physiology. Through various incidents, she has ended up this way, and she is making the most of things. But, no, you are not supposed to do anything. We can turn around and drop you back at the Forward Unto Dawn at any time you wish, though I believe you will find Galactic Federation Headquarters much more accommodating."

* * *

><p>Sorry about the lateness again! Once a year updates go? eh... ANYWAY On to some review responses.<p>

* * *

><p>"I didn't know what to expect going into this, considering how short the first chapter was. However, that was pretty good! Only complaints that I could make is that 1) The Varia Suit upgrade that Samus received in Fusion makes her immune to cold temperatures while she's in her suit. Considering Samus can't get out of her suit in this story, cold shouldn't be a problem. 2) Samus should be able to dematerialize her suit like she's been able to do in several games if she REALLY wants to take it off, so there's that. 3) Going off of what the creator of Metroid Fusion said(Yoshio Sakamoto), I think by absorbing the SA-X at the end of Fusion, Samus might be immune to cold now going off of this: "When she absorbed the core of the SAX (the perfect condition of Samus), she basically reconstituted her genetic condition. She didn't recover the physical damage of her amputated suit, but she did recover her genetic condition." 4) In the beginning of Fusion, when Samus received the Metroid vaccine, it completely killed and removed all X Parasites from her system, so saying that "the X Parasites that still inhabit my body" seems incorrect.<p>

Quick questions about going forward though. 1) Does Samus have the Omega Suit(the orange and yellow suit) that he had at the end of Fusion? 2) Is Samus going to have Adam's AI in her ship, because I don't see why she would get rid of that.

Like I said, this story seems pretty good so far, so I'm looking forward to what you do next."

I can adress the first parts fairly concisely in the simple fact that this is more of a "what if" scenario. I strove to give Samus and John their own strengths and weaknesses that I could develop outside the canonical ones. We'll see John get some cool new things in the upcoming chapters, just as a thing. I really appreciate the thought put into that review, though, and I thank you for reading.

As for the questions 1) Yes, that's the general look of the suit, though it's changed slightly in that it has the thorns in the palms. 2) Adam? The AI? That would be madness. Clearly I have put Joseph as the- No, yeah, it's Adam. Same ship, though I think at this point Samus is going to take the Adam AI with her from ship to ship. It's just more convenient than it is inconvenient.

* * *

><p>"I love the descriptions of the metroid vaccine affecting her and I'm curious to see if they will be friends or foes... Great job! Exciting to see more soon"<p>

THANK YOU! That's a wonderful thing to say! You're a good person. Erstwhile allies is the best you get for now, though.

* * *

><p>"Ah... I finally understand what's happening here. So Samus' recovery from the X parasite is a work in progress. It took me a while to realise that there more aspects of his story that are "divergents" of the canon storyline and what happens in it. Such as how Samus is reactingresponding to both the X parasite and its vaccine. It seems to suggest that the X parasite migt make a come back. There is a sense of foreboding/foreshadowing about it. Overall, I belive you have something here. Whatever it is has got me "stuck" to this story and eagery await for more updates. This story is quite unique; enough to make me fav and follow. Keep calm and keep it up."

Yeah, I'm really fond of alternate paths time could have taken. And i am quite glad to have stuck you. Might wanna grab that blue glowey thing on your back there.

* * *

><p>"OMG! Samus is basically an energy vampire ain't she?! OMG No Metroid story I've read (of which there are few) has ever made Samus into a vampire like creature! Maybe someone else has done it but this is just freaking AMAZING! XD By the Traveller this is good. XD<p>

PS: I'm reviewing chapters in reverse :3 Weird huh..."

YEAH! I've never seen it done like that either, and, honestly, it seemed a really logical step to me. She's basically turning into a Metroid. What are Metroids but blobby energy vampires? It's not even a three step process. But maybe it's just the weird way my mind works. WHO KNOWS?!

Also, yaya, you're weird. That's okay, though, weird is good.

* * *

><p>"I like the story but I hope the metroid mutations are a temporary thing,"<p>

Sorry, friend. That's one of the big themes of the story. I might as well take out Samus if I do that. And then John. And after that Cortana.


End file.
